Added xfail to tests that fail due to logging bug (#444)

* Added xfail to tests that fail due to logging bug

* Added more details to the xfail call

tests/napari/test_curation.py

@@ -24,6 +24,7 @@ def curation_widget(make_napari_viewer):
     return widget
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_add_new_training_layers(curation_widget):
     viewer = curation_widget.viewer
     layers = viewer.layers
@@ -38,6 +39,7 @@ def test_add_new_training_layers(curation_widget):
     assert layers[1].name == "Training data (non cells)"
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_cell_marking(curation_widget, tmp_path):
     """
     Check that marking cells and non-cells works as expected.
@@ -130,13 +132,15 @@ def valid_curation_widget(make_napari_viewer) -> CurationWidget:
     return curation_widget
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_check_image_data_for_extraction(valid_curation_widget):
     """
     Check valid curation widget has extractable data.
     """
     assert valid_curation_widget.check_image_data_for_extraction()
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_check_image_data_wrong_shape(valid_curation_widget):
     """
     Check curation widget shows expected user message if images don't have
@@ -156,6 +160,7 @@ def test_check_image_data_wrong_shape(valid_curation_widget):
         )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_check_image_data_missing_signal(valid_curation_widget):
     """
     Check curation widget shows expected user message if signal image is
@@ -170,12 +175,14 @@ def test_check_image_data_missing_signal(valid_curation_widget):
         )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_is_data_extractable(curation_widget, valid_curation_widget):
     """Check is_data_extractable works as expected."""
     assert not curation_widget.is_data_extractable()
     assert valid_curation_widget.is_data_extractable()
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_get_output_directory(valid_curation_widget):
     """Check get_output_directory returns expected value."""
     with patch(

tests/napari/test_detection.py

@@ -43,6 +43,7 @@ def test_detect_worker():
     worker.work()
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 @pytest.mark.parametrize(
     argnames="analyse_local",
     argvalues=[True, False],  # increase test coverage by covering both cases
@@ -67,6 +68,7 @@ def test_run_detect_without_inputs():
         assert show_info.called
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_reset_defaults(get_detect_widget):
     """Smoke test that restore defaults doesn't error."""
     get_detect_widget.reset_button.clicked()

tests/napari/test_training.py

@@ -23,6 +23,7 @@ def get_training_widget(make_napari_viewer):
     return widget
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_reset_to_defaults(get_training_widget):
     """
     A simple test for the reset button.
@@ -45,6 +46,7 @@ def test_reset_to_defaults(get_training_widget):
     assert get_training_widget.test_fraction.value == 0.10
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_run_with_no_yaml_files(get_training_widget):
     """
     Checks whether expected info message will be shown to user if they don't
@@ -57,6 +59,7 @@ def test_run_with_no_yaml_files(get_training_widget):
         )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_run_with_virtual_yaml_files(get_training_widget):
     """
     Checks that training is run with expected set of parameters.

tests/napari/test_utils.py

@@ -1,4 +1,5 @@
 import numpy as np
+import pytest
 from brainglobe_utils.cells.cells import Cell
 
 from cellfinder.napari.utils import (
@@ -10,6 +11,7 @@
 )
 
 
+@pytest.mark.xfail(reason="See discussion in #443", raises=AssertionError)
 def test_add_classified_layers(make_napari_viewer):
     """Smoke test for add_classified_layers utility"""
     cell_pos = [1, 2, 3]